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Rework pull request #489 memory handling to respect deployer set _JAVA_OPTIONS.

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As discussed here https://bitbucket.org/galaxy/galaxy-central/pull-request/489/srma-tool-requires-at-least-2048m-memory/diff. Thanks to Bjoern for input.
This commit is contained in:
John Chilton
2014-09-22 13:20:49 -04:00
parent 0a9d671f52
commit 34e1273f9b
1 changed files with 4 additions and 2 deletions
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tools/sr_mapping/srma_wrapper.py
+4 -2
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@@ -157,8 +157,10 @@ def __main__():
#create a temp output name, ending in .bam due to required naming conventions? unkown if required
output_bam_filename = os.path.join( tmp_dir, "%s.bam" % os.path.split( options.output )[-1] )
# generate commandline
cmd = 'java -Xmx2048m -jar %s I=%s O=%s R=%s %s' % ( os.path.join( options.jarBin, options.jarFile ), input_bam_filename, output_bam_filename, reference_filepath_name, srma_cmds )
java_opts = ''
if '_JAVA_OPTIONS' not in os.environ:
java_opts = '-Xmx2048m'
cmd = 'java %s -jar %s I=%s O=%s R=%s %s' % ( java_opts, os.path.join( options.jarBin, options.jarFile ), input_bam_filename, output_bam_filename, reference_filepath_name, srma_cmds )
# need to nest try-except in try-finally to handle 2.4
try:
try: